Tags: ReactionMechanismGenerator/RMG-Py
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RMG-Py release v3.3.0 ===================== Numbers like #0000 correspond to pull requests on GitHub. https://github.com/ReactionMechanismGenerator/RMG-Py/pulls?q=is%3Apr+is%3Aclosed RMG-Py Itself - Python 3.9 in #2741 - Removing the excessive debug comment in #2102 - Conversion from nose to pytest in #2516 - Modified main.py script to include TROE reactions in the violators log in #2614 - Replace a few packages maintained by us to their conda-forge version in #2624 - Switch muq, lpsolve55, and RingDecomposerLib from rmg to conda-forge in #2671 - environment.yml Unblocking Python 3.11 - rdkit to conda-forge channel, remove chemprop for now in #2553 - Make chemkin read of transport and thermo files more robust in #2643 - Add documentation about speciesCuttingThreshold in #2601 - Fix Failing Joback Method Unit Test in #2682 - Load a kinetic library not in the RMG database in #2663 - Draw reversible arrow if reaction is reversible in #2693 - Ignore more example output files in git. in #2822 - Make RMG-Py conda Work Again in #2820 - fix typos in #2670 - update user and developer installation instructions to point towards miniforge in #2719 - Add and improve to_cantera methods for conversion to in-memory Cantera objects in #2700 - Add details to thermo comments. in #2788 - A note about installing developer version from Docker. in #2806 Bug Fixes - When loading all reaction libraries, only process "reactions.py" files. in #2513 - Fix pytest Discovery Bug (FooTest vs. TestFoo), Add Missing Tests, Fix Generator Tests in #2525 - Minor: Added quotation marks to Pt111 in the docs in #2529 - Fix Failing CI because of cclib in #2535 - Update RMSE/MAE average formula for BAC cross validation in #2538 - Fix a logical short circuit in a test expression in #2542 - FIX: Updated logical expression to remove short circuit in #2555 - Fix CC smiles in #2545 - changing forbidden groups documentation in #2561 - exempt announcements from being closed as stale in #2565 - Update uncertainty SI when averaging ThermoData in #2589 - Julia restriction in #2609 - changed typo from pydas.daspk to pydas.dassl #2070 in #2615 - restrict newer versions of cclib in #2638 - Remove duplicated test data directory in #2644 - FIx Handling of Initial Species with Seed Mechanisms in #2653 - add check for all zeros in thermo comparison in #2658 - Better debugging messages for database errors. in #2661 - Send P in SI units to Chebyshev.fit_to_data() when reversing a rate in #2662 - Draw Hydrogen bonds (again) in #2734 - Fix library reaction barrier heights for linear scaling in #2729 - Fix database issues with loading new kinetic libraries in #2753 - Update comment parser for autogen trees in #2787 - New Features (and their fixes) Electrochemistry - Electrochemistry! (finally) a.k.a. RMG-electrocat in #2598 - Fix bug in electrons initialization for depository reaction data in #2775 Automated Fragment Modeling - Remove label in adjlist before detecting cutting label in #2519 - Add regression input file for fragment + simple reactor and regression test for fragment + RMS reactor in #2571 - Compatibility of regression.py with fragment in #2574 - fragment.py: refactoring, patches, and compatibility with RMS in #2413 - Add Fragment Reattachment Example Notebook in #2585 - Fix Fragment Resonance Structure Bug in #2647 - Fix AFM fragment crash in LiquidReactor in #2813 Surface Catalysis - Doc surf rxns in #2497 - correcting bidentate adsorption rate constant in #2533 - fix Kc for bidentate rxns in #2554 - Group Structures for Complex Surface Representations in #2618 - Patch for surface regression diffmodels in #2656 - Add surface combustion example for regression testing in #2514 - adding resonance for adsorbates in #2511 AECs and BACs - Allow user to plot correlation matrix for AECs in #2550 Arkane - Add keyword "HF=" to parse electronic energy in #2586 - resolved issue #2266 in #2651 - Allow scratch dir as input for arkane symmetry calculation in #2691 - Change method for loading energies from Gaussian log files to regex search to avoid errors in #2595 - updating 'rotconsts' ref to be compatible with cclib v1.8+ in #2639 - Process monoatomic molecules in Arkane's Orca ESS adapter in #2709 - Parse RS2C (CASPT2) energy in Molpro in #2711 - Fxi UnboundLocalError: local variable 'e_electronic_with_corrections' referenced before assignment in #2756 - Fix rotational constants in Gaussian files listing ****s in #2761 - Orca parser fixup in #2739 - Molpro f12a in #2771 - Fix CCSD(T)-F12 energy parsing in #2816 Deprecations - Remove kinetic group additivity methods from code and documentation in #2612 - Clean up some code for calculating degeneracy in kinetics codebase in #2632 - Remove Wiki and gitter from README in #2762 - [Docs] Update outdated docs, wiki, and contributor guidelines in #2703 Continuous Integration - Fix CI workflow to function on forked pushes. in #2515 - Tweak annotation workflow name. in #2517 - Instruct Docker, Github Actions, and users to use 'for_rmg' branch of RMS in #2523 - update docker usage instructions to point to v3.2.0 in #2522 - Switch back to RMS main in CI in #2552 - Change Documentation Build Action to use github-actions bot instead of RMG_dev in #2599 - fix checkout command for docs building action in #2602 - Continuous Integration, Documentation Build, and Dockerfile Fixes in #2608 - Continued docs build fixes in #2610 - documentation builder bug fixes and general overhaul in #2621 - GitHub Actions Maintenance in #2628 - github actions CI maintainence in #2669 - Remove default Channel from environment.yml in #2712 - Patch minimal_surface Regression Test in #2674 - Change CI to use Miniforge3 instead of Mambaforge - Deprecate the nomkl mutex metapackage in #2723 - Changed Dockerfile to use Miniforge3 - Update CI artifact actions to v4 and fix runner glitch in #2748 - require a more recent version of mkl for Cantera in #2766 - Fix the CI regression logging; make Julia optional via environment and module variables. in #2802 - Lazy loading of Julia things in #2804 - Docker build updates in #2808
This is where the 'cat' branch (for RMG-Cat, the fork dealing with heterogeneous catalysis) was when it was finally merged to RMG master. The route merged to master is much cleaner, having undergone *extensive* interactive rebasing. The route leading up to this tag, is the more honest history, warts and all. From now on, development should continue on the master branch.
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